Added patches from #212689, #232292 and #246414 to ebuilds for ghemical-2.95 and 2.98. --- sci-chemistry/ghemical/ChangeLog | 18 +++++ sci-chemistry/ghemical/Manifest | 12 +++ .../files/ghemical-2.95-g_threads-246414.patch | 26 +++++++ .../files/ghemical-2.95-import_export-212689.patch | 54 ++++++++++++++ .../ghemical-2.95-libf2c_config_test-232292.patch | 13 ++++ .../files/ghemical-2.98-import_export-212689.patch | 54 ++++++++++++++ .../ghemical-2.98-libf2c_config_test-232292.patch | 13 ++++ sci-chemistry/ghemical/files/ghemical-gcc43.patch | 14 ++++ sci-chemistry/ghemical/ghemical-2.95.ebuild | 74 ++++++++++++++++++++ sci-chemistry/ghemical/ghemical-2.98.ebuild | 74 ++++++++++++++++++++ sci-chemistry/ghemical/metadata.xml | 21 ++++++ 11 files changed, 373 insertions(+), 0 deletions(-) create mode 100644 sci-chemistry/ghemical/ChangeLog create mode 100644 sci-chemistry/ghemical/Manifest create mode 100644 sci-chemistry/ghemical/files/ghemical-2.95-g_threads-246414.patch create mode 100644 sci-chemistry/ghemical/files/ghemical-2.95-import_export-212689.patch create mode 100644 sci-chemistry/ghemical/files/ghemical-2.95-libf2c_config_test-232292.patch create mode 100644 sci-chemistry/ghemical/files/ghemical-2.98-import_export-212689.patch create mode 100644 sci-chemistry/ghemical/files/ghemical-2.98-libf2c_config_test-232292.patch create mode 100644 sci-chemistry/ghemical/files/ghemical-gcc43.patch create mode 100644 sci-chemistry/ghemical/ghemical-2.95.ebuild create mode 100644 sci-chemistry/ghemical/ghemical-2.98.ebuild create mode 100644 sci-chemistry/ghemical/metadata.xml
diff --git a/sci-chemistry/ghemical/ChangeLog b/sci-chemistry/ghemical/ChangeLog new file mode 100644 index 0000000..012896a --- /dev/null +++ b/sci-chemistry/ghemical/ChangeLog @@ -0,0 +1,18 @@ +# ChangeLog for sci-chemistry/ghemical +# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*ghemical-2.98 (06 Feb 2009) +*ghemical-2.95 (06 Feb 2009) + + 06 Feb 2009; Reinis Danne <[email protected]> + +files/ghemical-2.95-g_threads-246414.patch, + +files/ghemical-2.95-import_export-212689.patch, + +files/ghemical-2.95-libf2c_config_test-232292.patch, + +files/ghemical-2.98-import_export-212689.patch, + +files/ghemical-2.98-libf2c_config_test-232292.patch, + +files/ghemical-gcc43.patch, +metadata.xml, +ghemical-2.95.ebuild, + +ghemical-2.98.ebuild: + Added patches from #212689, #232292 and #246414 to ebuilds for + ghemical-2.95 and 2.98. + diff --git a/sci-chemistry/ghemical/Manifest b/sci-chemistry/ghemical/Manifest new file mode 100644 index 0000000..a281a40 --- /dev/null +++ b/sci-chemistry/ghemical/Manifest @@ -0,0 +1,12 @@ +AUX ghemical-2.95-g_threads-246414.patch 553 RMD160 d06e847c0c2f4c445b3e73b624cd81ccec4589b2 SHA1 d523d4e092aaa79581bffeb11283c685065117f0 SHA256 e5bf7ceed065218397b9611c24a390f0ed96ce485a29e945095092dbe38ef188 +AUX ghemical-2.95-import_export-212689.patch 1288 RMD160 abbbce698c8f2eff1e4c35224ccccd8e7411d20b SHA1 5edb4c1f951d0dc6724f78bf5b6a9a544f8c7be7 SHA256 fc487c38e8ac30c2936781aa194b57a2d7f5621ea9af484b7ab734b5dbd819bd +AUX ghemical-2.95-libf2c_config_test-232292.patch 321 RMD160 366614a65c978602af23d7d8ed3c4135bc226ef5 SHA1 cca2e3cc88ec4d38c4e55a5c3a368e0a62a5cd25 SHA256 3497cdf758fac1aa207f1bb7fca9621e2145402ca346bc5406fff49b6d570a33 +AUX ghemical-2.98-import_export-212689.patch 1288 RMD160 abbbce698c8f2eff1e4c35224ccccd8e7411d20b SHA1 5edb4c1f951d0dc6724f78bf5b6a9a544f8c7be7 SHA256 fc487c38e8ac30c2936781aa194b57a2d7f5621ea9af484b7ab734b5dbd819bd +AUX ghemical-2.98-libf2c_config_test-232292.patch 321 RMD160 366614a65c978602af23d7d8ed3c4135bc226ef5 SHA1 cca2e3cc88ec4d38c4e55a5c3a368e0a62a5cd25 SHA256 3497cdf758fac1aa207f1bb7fca9621e2145402ca346bc5406fff49b6d570a33 +AUX ghemical-gcc43.patch 403 RMD160 7ed2b8633e0ec98024e97417cd1751cea2a33a96 SHA1 bcb7336fddf379c202abc61a8423d5c9f9be8d91 SHA256 de2ed1a0190a5fb450c88217fa88c62b99c6243c3547776e0f806c1acd0b0630 +DIST ghemical-2.95.tar.gz 2062097 RMD160 866cb26b7980d9cdfc1f73ddc03240df583ded20 SHA1 ac9419292554103f2b9bc7be8dfc921906134351 SHA256 1083bd02aba1a73fe7008a2f23d1b974147ac95f34f7ef2f90d8d2f9a823e8cc +DIST ghemical-2.98.tar.gz 2065429 RMD160 836e1ec7a45615b58aa4a369d2fc21f5d599fbf4 SHA1 d4212aefe12b4d1f98ce6859e0f0d0a658c64a5d SHA256 2163b321df97698487017d32df77fdf4a9afb385b60f93145fd161a277c7ae82 +EBUILD ghemical-2.95.ebuild 1916 RMD160 c7a1581f426a168184f921b2eec056c3d0bb40f5 SHA1 e8d04b780e343e1415124e30a77d5f54db7e0bee SHA256 48f3967160544ba1cc7a3482d231799e87ef22c5791d0da8101f196878c496c0 +EBUILD ghemical-2.98.ebuild 1903 RMD160 c07a4268703e34f60a0a44d9349840c2e45afa79 SHA1 4094546e55523b25b27c0f916e6f468bf75b3659 SHA256 a34a7731d61fa9a2c66d4d73ec92a59780ccd04cac5ae9d26b591d80e7d760bc +MISC ChangeLog 677 RMD160 d2aa468f0f2e0661a23fcd9b15d220d08ef4f98d SHA1 857d6eeb3649eeaac8bb82c860d931449f56ff9f SHA256 c6abeb4834485ac321c5a32c6fe4c80785b45434ad8478dbc6727d0c7781a0ea +MISC metadata.xml 917 RMD160 5ada96e4b3d836e6525a5613076ea6da69e5daec SHA1 bcaf353e9ba29dfa292785049d643f798e46f24a SHA256 3400c4d52b6b7864856cca423c808bbec063fe565bf570411283d66af3771a70 diff --git a/sci-chemistry/ghemical/files/ghemical-2.95-g_threads-246414.patch b/sci-chemistry/ghemical/files/ghemical-2.95-g_threads-246414.patch new file mode 100644 index 0000000..7e2c594 --- /dev/null +++ b/sci-chemistry/ghemical/files/ghemical-2.95-g_threads-246414.patch @@ -0,0 +1,26 @@ +--- src/gtk_main.cpp.orig 2007-05-23 14:21:19.000000000 +0300 ++++ src/gtk_main.cpp 2008-11-11 17:53:02.000000000 +0200 +@@ -33,6 +33,13 @@ + + int main(int argc, char ** argv) + { ++#ifdef ENABLE_THREADS ++ ++ g_thread_init(NULL); ++ gdk_threads_init(); ++ ++#endif // ENABLE_THREADS ++ + GError * error = NULL; + + GOptionContext * option_context = g_option_context_new("- a GTK2 molecular modelling program"); +@@ -46,9 +53,6 @@ + + #ifdef ENABLE_THREADS + +- g_thread_init(NULL); +- gdk_threads_init(); +- + gdk_threads_enter(); + + #endif // ENABLE_THREADS diff --git a/sci-chemistry/ghemical/files/ghemical-2.95-import_export-212689.patch b/sci-chemistry/ghemical/files/ghemical-2.95-import_export-212689.patch new file mode 100644 index 0000000..b643eb6 --- /dev/null +++ b/sci-chemistry/ghemical/files/ghemical-2.95-import_export-212689.patch @@ -0,0 +1,54 @@ +--- src/project.cpp 2007-08-16 11:20:00.000000000 +0200 ++++ src/project.cpp 2008-11-10 21:39:15.000000000 +0200 +@@ -307,6 +307,12 @@ + ifstream ifile; + ostringstream intermed; + file_trans translator; ++ ++ // Store the current locale and switch to "C" ++ ++ static char my_num_locale[32] = "C"; ++ strcpy(my_num_locale, setlocale(LC_NUMERIC, NULL)); ++ setlocale(LC_NUMERIC, "C"); + + if (index == 0) // Automatic detection + { +@@ -328,7 +334,13 @@ + } + + istringstream interInput(intermed.str()); +- return ReadGPR((* this), interInput, false); ++ bool retval = ReadGPR((* this), interInput, false); ++ ++ // Change back to the original locale ++ ++ setlocale(LC_NUMERIC, my_num_locale); ++ ++ return retval; + } + + bool project::ExportFile(const char * filename, int index) +@@ -337,6 +349,12 @@ + stringstream intermed; + file_trans translator; + ++ // Store the current locale and switch to "C" ++ ++ static char my_num_locale[32] = "C"; ++ strcpy(my_num_locale, setlocale(LC_NUMERIC, NULL)); ++ setlocale(LC_NUMERIC, "C"); ++ + WriteGPR_v100((* this), intermed); // this is for openbabel-1.100.2 + istringstream interInput(intermed.str()); + +@@ -359,6 +377,10 @@ + ofile.close(); + } + ++ // Change back to the original locale ++ ++ setlocale(LC_NUMERIC, my_num_locale); ++ + return true; + } + diff --git a/sci-chemistry/ghemical/files/ghemical-2.95-libf2c_config_test-232292.patch b/sci-chemistry/ghemical/files/ghemical-2.95-libf2c_config_test-232292.patch new file mode 100644 index 0000000..c847e9e --- /dev/null +++ b/sci-chemistry/ghemical/files/ghemical-2.95-libf2c_config_test-232292.patch @@ -0,0 +1,13 @@ +--- configure.ac.orig 2008-07-17 22:34:51.000000000 -0400 ++++ configure.ac 2008-07-17 22:35:56.000000000 -0400 +@@ -83,6 +83,9 @@ + + AC_CHECK_LIB(X11,XOpenDisplay,,[AC_MSG_ERROR([X11 library missing])]) + ++## Need libf2c for MOPAC ++AC_CHECK_LIB(f2c,i_len) ++ + ## are the rest necessary??? + + AC_CHECK_LIB(Xmu,XmuDrawLogo) + diff --git a/sci-chemistry/ghemical/files/ghemical-2.98-import_export-212689.patch b/sci-chemistry/ghemical/files/ghemical-2.98-import_export-212689.patch new file mode 100644 index 0000000..b643eb6 --- /dev/null +++ b/sci-chemistry/ghemical/files/ghemical-2.98-import_export-212689.patch @@ -0,0 +1,54 @@ +--- src/project.cpp 2007-08-16 11:20:00.000000000 +0200 ++++ src/project.cpp 2008-11-10 21:39:15.000000000 +0200 +@@ -307,6 +307,12 @@ + ifstream ifile; + ostringstream intermed; + file_trans translator; ++ ++ // Store the current locale and switch to "C" ++ ++ static char my_num_locale[32] = "C"; ++ strcpy(my_num_locale, setlocale(LC_NUMERIC, NULL)); ++ setlocale(LC_NUMERIC, "C"); + + if (index == 0) // Automatic detection + { +@@ -328,7 +334,13 @@ + } + + istringstream interInput(intermed.str()); +- return ReadGPR((* this), interInput, false); ++ bool retval = ReadGPR((* this), interInput, false); ++ ++ // Change back to the original locale ++ ++ setlocale(LC_NUMERIC, my_num_locale); ++ ++ return retval; + } + + bool project::ExportFile(const char * filename, int index) +@@ -337,6 +349,12 @@ + stringstream intermed; + file_trans translator; + ++ // Store the current locale and switch to "C" ++ ++ static char my_num_locale[32] = "C"; ++ strcpy(my_num_locale, setlocale(LC_NUMERIC, NULL)); ++ setlocale(LC_NUMERIC, "C"); ++ + WriteGPR_v100((* this), intermed); // this is for openbabel-1.100.2 + istringstream interInput(intermed.str()); + +@@ -359,6 +377,10 @@ + ofile.close(); + } + ++ // Change back to the original locale ++ ++ setlocale(LC_NUMERIC, my_num_locale); ++ + return true; + } + diff --git a/sci-chemistry/ghemical/files/ghemical-2.98-libf2c_config_test-232292.patch b/sci-chemistry/ghemical/files/ghemical-2.98-libf2c_config_test-232292.patch new file mode 100644 index 0000000..c847e9e --- /dev/null +++ b/sci-chemistry/ghemical/files/ghemical-2.98-libf2c_config_test-232292.patch @@ -0,0 +1,13 @@ +--- configure.ac.orig 2008-07-17 22:34:51.000000000 -0400 ++++ configure.ac 2008-07-17 22:35:56.000000000 -0400 +@@ -83,6 +83,9 @@ + + AC_CHECK_LIB(X11,XOpenDisplay,,[AC_MSG_ERROR([X11 library missing])]) + ++## Need libf2c for MOPAC ++AC_CHECK_LIB(f2c,i_len) ++ + ## are the rest necessary??? + + AC_CHECK_LIB(Xmu,XmuDrawLogo) + diff --git a/sci-chemistry/ghemical/files/ghemical-gcc43.patch b/sci-chemistry/ghemical/files/ghemical-gcc43.patch new file mode 100644 index 0000000..93557d4 --- /dev/null +++ b/sci-chemistry/ghemical/files/ghemical-gcc43.patch @@ -0,0 +1,14 @@ +--- src-orig/pangofont_wcl.cpp 2008-11-30 16:15:23.932475487 -0600 ++++ src/pangofont_wcl.cpp 2008-11-30 16:16:09.620396370 -0600 +@@ -22,6 +22,10 @@ + + #include <gtk/gtkgl.h> + ++#include <string.h> ++ ++#include <cstdlib> ++using namespace std; + /*################################################################################################*/ + + pangofont_wcl::pangofont_wcl(ogl_camera * cam) : + diff --git a/sci-chemistry/ghemical/ghemical-2.95.ebuild b/sci-chemistry/ghemical/ghemical-2.95.ebuild new file mode 100644 index 0000000..63b6fbd --- /dev/null +++ b/sci-chemistry/ghemical/ghemical-2.95.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +inherit eutils flag-o-matic autotools + +DESCRIPTION="Chemical quantum mechanics and molecular mechanics" +HOMEPAGE="http://bioinformatics.org/ghemical/"; + +SRC_URI="http://bioinformatics.org/ghemical/download/current/${P}.tar.gz"; +LICENSE="GPL-2" + +SLOT="0" + +KEYWORDS="~amd64 ~x86" +IUSE="threads openbabel seamonkey" +RDEPEND="virtual/glut + virtual/glu + virtual/opengl + sci-chemistry/mpqc + x11-libs/libICE + x11-libs/libSM + x11-libs/libX11 + x11-libs/libXext + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXt + x11-libs/pango + >=x11-libs/gtk+-2.6 + >=x11-libs/gtkglext-1.0.5 + >=gnome-base/libglade-2.4 + >=sci-libs/libghemical-2.96 + >=x11-libs/liboglappth-0.96 + openbabel? ( >=sci-chemistry/openbabel-2 ) + threads? ( >=dev-libs/glib-2.4 )" + +DEPEND="${RDEPEND} + >=dev-util/pkgconfig-0.15" + +src_unpack() { + unpack ${A} + cd "${S}" + + epatch "${FILESDIR}/${P}-import_export-212689.patch" || die "Faild to apply ${P}-import_export-212689.patch" + epatch "${FILESDIR}/${P}-libf2c_config_test-232292.patch" || die "Failed to apply ${P}-libf2c_config_test-232292.patch" + epatch "${FILESDIR}/${P}-g_threads-246414.patch" || die "Failed to apply ${P}-g_threads-246414.patch" + + eautoreconf +} + +src_compile() { + +# With amd64, if you want gamess I recommend adding gamess and gtk-gamess to package.provided for now. + +# Change the built-in help browser. + if use seamonkey ; then + sed -i -e 's|mozilla|seamonkey|g' src/gtk_app.cpp || die "sed failed for seamonkey!" + else + sed -i -e 's|mozilla|firefox|g' src/gtk_app.cpp || die "sed failed for seamonkey!" + fi + + # For libf2c + append-ldflags -Xlinker -defsym -Xlinker MAIN__=main + + econf \ + $(use_enable openbabel) \ + $(use_enable threads) \ + || die "configure failed" + emake || die "make failed" +} + +src_install() { + emake DESTDIR="${D}" install || die "install failed" +} diff --git a/sci-chemistry/ghemical/ghemical-2.98.ebuild b/sci-chemistry/ghemical/ghemical-2.98.ebuild new file mode 100644 index 0000000..c07d72c --- /dev/null +++ b/sci-chemistry/ghemical/ghemical-2.98.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +inherit eutils flag-o-matic autotools + +DESCRIPTION="Chemical quantum mechanics and molecular mechanics" +HOMEPAGE="http://bioinformatics.org/ghemical/"; + +SRC_URI="http://bioinformatics.org/ghemical/download/current/${P}.tar.gz"; +LICENSE="GPL-2" + +SLOT="0" + +KEYWORDS="~amd64 ~x86" +IUSE="threads openbabel seamonkey" +RDEPEND="virtual/glut + virtual/glu + virtual/opengl + sci-chemistry/mpqc + x11-libs/libICE + x11-libs/libSM + x11-libs/libX11 + x11-libs/libXext + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXt + x11-libs/pango + >=x11-libs/gtk+-2.6 + >=x11-libs/gtkglext-1.0.5 + >=gnome-base/libglade-2.4 + >=sci-libs/libghemical-2.96 + >=x11-libs/liboglappth-0.96 + openbabel? ( >=sci-chemistry/openbabel-2 ) + threads? ( >=dev-libs/glib-2.4 )" + +DEPEND="${RDEPEND} + >=dev-util/pkgconfig-0.15" + +src_unpack() { + unpack ${A} + cd "${S}" + + epatch "${FILESDIR}/ghemical-gcc43.patch" || die "Failed to apply ghemical-gcc43.patch" + epatch "${FILESDIR}/${P}-import_export-212689.patch" || die "Failed to apply ${P}-import_export-212689.patch" + epatch "${FILESDIR}/${P}-libf2c_config_test-232292.patch" || die "Failed to apply ${P}-libf2c_config_test-232292.patch" + + eautoreconf +} + +src_compile() { + +# With amd64, if you want gamess I recommend adding gamess and gtk-gamess to package.provided for now. + +# Change the built-in help browser. + if use seamonkey ; then + sed -i -e 's|mozilla|seamonkey|g' src/gtk_app.cpp || die "sed failed for seamonkey!" + else + sed -i -e 's|mozilla|firefox|g' src/gtk_app.cpp || die "sed failed for seamonkey!" + fi + + # For libf2c + append-ldflags -Xlinker -defsym -Xlinker MAIN__=main + + econf \ + $(use_enable openbabel) \ + $(use_enable threads) \ + || die "configure failed" + emake || die "make failed" +} + +src_install() { + emake DESTDIR="${D}" install || die "install failed" +} diff --git a/sci-chemistry/ghemical/metadata.xml b/sci-chemistry/ghemical/metadata.xml new file mode 100644 index 0000000..9627988 --- /dev/null +++ b/sci-chemistry/ghemical/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> +<herd>sci-chemistry</herd> +<longdescription> +Ghemical supports both quantum-mechanics (semi-empirical and ab initio) models +and molecular mechanics models (there is an experimental Tripos 5.2-like force +field for organic molecules). Also a tool for reduced protein models is +included. Geometry optimization, molecular dynamics and a large set of +visualization tools are currently available. +</longdescription> +<use> + <flag name='gamess'>Add GAMESS interface for QM/MM + (<pkg>sci-chemistry/gamess</pkg>)</flag> + <flag name='mopac7'>Apply compilation fix for + <pkg>sci-chemistry/mopac7</pkg> support</flag> + <flag name='openbabel'>Use <pkg>sci-chemistry/openbabel</pkg> for file + conversions</flag> + <flag name='toolbar'>Build the shortcuts toolbar</flag> +</use> +</pkgmetadata> -- 1.6.0.6
